The Validation page summarizes the results of false discovery rate (FDR) calculations in the processing and consensus workflows. The application calculates the FDR values for PSMs, peptide groups, proteins, and protein groups if the corresponding items are available in the report.
- For protein groups, proteins, and peptide groups, the Validation Summary summarizes and displays the results of the FDRs calculated on the basis of the number of these items in the results report.
- For PSMs, the Validation Summary summarizes and displays FDRs calculated on the basis of concatenated PSMs from target and decoy FASTA files. For validation purposes, it also shows the score thresholds used to assign peptide confidences.
For more information on the calculation of FDRs, see Validating results.
After you create the results report, you cannot change the FDR values.
The Validation page consists of the following four subpages:
- Consensus Step Validation page: Displays the settings of the Peptide Validator node parameters used in the consensus workflow. It displays the parameters by the category displayed on the Parameters page of the Workflow Editor, not by parameter name.
- Processing Step Validation page: Displays the details of the FDR calculations for the PSMs identified by a single search node in one processing results file. It groups the detailed results of the FDR calculation by the different processing results (MSF) files. For each search node in the processing workflow of the file, it reports the following information:
- The type of FDR calculation performed. Depending on the validation node used and its parameter settings, the Processing Step Validation page displays different messages about the type of FDR calculation used:
- If you included the Fixed Value PSM Validator node in the processing workflow, the Processing Step Validation page indicates that the application performed no decoy search and set PSM confidences according to fixed threshold values.
- If you included the Target Decoy PSM Validator node in the processing workflow, the Processing Step Validation page indicates the setting of the node’s Concatenated FDR Calculation parameter, which determines whether the application used the separated calculation method or the concatenated calculation method to calculate the FDRs.
- If you included the Percolator node in the processing workflow, the Processing Step Validation page indicates that the application performed the FDR calculation according to the Percolator node’s algorithms. For information on the Percolator node, see the Percolator node in the Proteome Discoverer Help.
- A summary of the FDR rate and the score thresholds used to assign the PSM confidences to the PSMs identified by the corresponding search node. The Processing Step Validation page reports the details separately for high-confidence and medium-confidence PSMs. Each part begins with the search node score used to calculate the FDR values and to assign PSM confidences. Next, the Processing Step Validation page reports the actual FDR for the target rate and the number of target and decoy PSMs passing the thresholds. At the end of each section is a detailed list of the search-engine-specific score thresholds used for calculating the FDR and for assigning confidences to the PSMs. If you use Percolator to assign confidences, the Processing Step Validation page reports the thresholds for the value selected to assign peptide confidences, followed by detailed Percolator output.
- Filters and Counts page: Displays the defined display filters and the number of filtered, total, and included result items on the following pages of the result file: Protein Groups, Proteins, Peptide Groups, PSMs, MS/MS Spectrum Info, Decoy Protein Groups, Decoy Proteins, Decoy Peptide Groups, and Decoy PSMs. Included result items are those not filtered out by the Peptide in Protein Annotation node and the Protein Grouping node.
- FDR Values (FDR Values for Entire Result) page: Displays the FDR values found for protein groups, proteins, peptide groups, and PSMs before the application applied any display filters.
